Best How To :

Are you sure your newick tree has named internal nodes? If not, try without passing any value to the format argument.

Also, please make sure that the filename is either absolute path to the file, or if its relative path , for example a.nwk , then make sure the file exists in the directory from which you are running the python script.

a. It's a left shift: https://docs.python.org/2/reference/expressions.html#shifting-operations It shifts the bits one to the left. b. Note that ^ is not the "to the power of" but "bitwise XOR" in Python. c. As the comment states: it defines "number of bits per signature" as 2**10 → 1024 d. The lines calculate...

I think the problem is with your start.py file. You have a function refreshgui which re imports start.py import will run every part of the code in the file. It is customary to wrap the main functionality in an ''if __name__ == '__main__': to prevent code from being run on...

This is a bug in Spring Integration; I have opened a JIRA Issue. if (variables != null) { result = scriptEngine.eval(script, new SimpleBindings(variables)); } else { result = scriptEngine.eval(script); } When the first branch of the if test is taken, the result variable is added to the SimpleBindings object, and...

if you only need to do this for a handful of points, you could do something like this. If intensites and radius are numpy arrays of your data: bin_width = 0.1 # Depending on how narrow you want your bins def get_avg(rad): average_intensity = intensities[(radius>=rad-bin_width/2.) & (radius<rad+bin_width/2.)].mean() return average_intensities #...

Afraid I don't know much about python, but I can probably help you with the algorithm. The encoding process repeats the following: multiply the current total by 17 add a value (a = 1, b = 2, ..., z = 26) for the next letter to the total So at...

I don't know what you are exactly trying to achieve but if you are trying to count R and K in the string there are more elegant ways to achieve it. But for your reference I had modified your code. N = int(raw_input()) s = [] for i in range(N):...

If you want the None and '' values to appear last, you can have your key function return a tuple, so the list is sorted by the natural order of that tuple. The tuple has the form (is_none, is_empty, value); this way, the tuple for a None value will be...

Just use photoshop or G.I.M.P.. I assure you, doing it that way will be much simpler and less redundant than essentially getting Tkinter to photo edit for you (not to mention what you're talking about is just bad practice when it comes to coding) Anyways, I guess if you really...

Your first problem is C++ name mangling. If you run nm on your .so file you will get something like this: nm test.so 0000000000000f40 T __Z3funv U _printf U dyld_stub_binder If you mark it as C style when compiled with C++: #ifdef __cplusplus extern "C" char fun() #else char fun(void)...

After updating your .bashrc, perform source ~/.bashrc to apply the changes. Also, merge the two BONSAI-related calls into one: export BONSAI=/home/me/Utils/bonsai_v3.2 UPDATE: It was actually an attempt to update the environment for some Eclipse-based IDE. This is a different usecase altogether. It should be described in the Eclipse help. Also,...

Don't call np.delete in a loop. It would be quicker to use boolean indexing: In [6]: A[X.astype(bool).any(axis=0)] Out[6]: array([[3, 4, 5]]) X.astype(bool) turns 0 into False and any non-zero value into True: In [9]: X.astype(bool).any(axis=0) Out[9]: array([False, True, False], dtype=bool) the call to .any(axis=0) returns True if any value in...

You might want to have a look at Tornado. It is well-documented and features built-in support for WebSockets. If you want to steer clear of the Tornado-framework, there are several Python implementations of Socket.io. Good luck!...

You can create a set holding the different IDs and then compare the size of that set to the total number of quests. The difference tells you how many IDs are duplicated. Same for names. Something like this (untested): def test_quests(quests): num_total = len(quests) different_ids = len(set((q.ID for q in...

Try ...where(SomeTable.BIN.in_(big_list)) PeeWee has restrictions as to what can be used in their where clause in order to work with the library. http://docs.peewee-orm.com/en/latest/peewee/querying.html#query-operators...

The convention is to declare constants in modules as variables written in upper-case (Python style guide: https://www.python.org/dev/peps/pep-0008/#global-variable-names). But there's no way to prevent someone else to re-declare such a variable -- thus ignoring conventions -- when importing a module. There are two ways of working around this when importing modules...

Your list contains one dictionary you can access the data inside like this : >>> yourlist[0]["popularity"] 2354 [0] for the first item in the list (the dictionary). ["popularity"] to get the value associated to the key 'popularity' in the dictionary....

Make sure you have set properly with ~/.boto and connect to aws, have the boto module ready in python. If not, go through this first: Getting Started with Boto For example, you need assign a new EIP 54.12.23.34 to the instance i-12345678 Make sure, EIP has been allocated(existed) and you...

Is it possible to use a variable in the AssignFile command? Yes. The second parameter of AssignFile has type string. The expression cFileDir + '\' + sFile has type string. FWIW, AssignFile is known as a function rather than a command. Getting on top of terminology like this will...

First off, it might not be good to just go by recall alone. You can simply achieve a recall of 100% by classifying everything as the positive class. I usually suggest using AUC for selecting parameters, and then finding a threshold for the operating point (say a given precision level)...

Twilio developer evangelist here. Twilio Client uses WebRTC and falls back to Flash in order to make web browsers into phones. Unfortunately Safari on iOS supports neither WebRTC nor Flash so Twilio Client cannot work within any browser on iOS. It is possible to build an iOS application to use...

To count how often one value occurs and at the same time you want to select those values, you'd simply select those values and count how many you selected: fruits = [f for f in foods if f[0] == 'fruit'] fruit_count = len(fruits) If you need to do this for...

about the deadlock: It is safe to use stdout=PIPE and wait() together iff you read from the pipe. .communicate() does the reading and calls wait() for you about the memory: if the output can be unlimited then you should not use .communicate() that accumulates all output in memory. what...

The explode function is being used correctly, so your problem is further up. Either $data[$i] = mysql_result($result,$i,"data"); isn't returning the expected string "2015-06-04" from the database OR your function $data[$i] = data_eng_to_it_($data[$i]); isn't returning the expected string "04 June 2015" So test further up by echo / var_dump after both...

You don't need to populate the variable, initializing it with a type declaration sets it to a default value (0 for ints, 0.0 for floats, and "" for strings). In general it's good practice to assign in place when the initial variable is meaningful: string $topCamera = "|top|topShape"; but it's...

Check the code before the print line for errors. This can be caused by an error in a previous line; for example: def x(): y = [ print "hello" x() This produces the following error: File "E:\Python\test.py", line 14 print "hello" ^ SyntaxError: invalid syntax When clearly the error is...

You need to read one bite per iteration, analyze it and then write to another file or to sys.stdout. Try this code: mesh = open("file.mesh", "r") mesh_out = open("file-1.mesh", "w") c = mesh.read(1) if c: mesh_out.write("{") else: exit(0) while True: c = mesh.read(1) if c == "": break if c...

Insert only accepts a final document or an array of documents, and an optional object which contains additional options for the collection. db.collection.insert( <document or array of documents>, { // options writeConcern: <document>, ordered: <boolean> } ) You may want to add the _id to the document in advance, but...

According to documentation of numpy.reshape , it returns a new array object with the new shape specified by the parameters (given that, with the new shape, the amount of elements in the array remain unchanged) , without changing the shape of the original object, so when you are calling the...

The pipeline calls transform on the preprocessing and feature selection steps if you call pl.predict. That means that the features selected in training will be selected from the test data (the only thing that makes sense here). It is unclear what you mean by "apply" here. Nothing new will be...

By default variables are string in Robot. So your first two statements are assigning strings like "xx,yy" to your vars. Then "evaluate" just execute your statement as Python would do. So, adding your two strings with commas will produce a list: $ python >>> 1,2+3,4 (1, 5, 4) So you...

Short answer: your correct doesn't work. Long answer: The binary floating-point formats in ubiquitous use in modern computers and programming languages cannot represent most numbers like 0.1, just like no terminating decimal representation can represent 1/3. Instead, when you write 0.1 in your source code, Python automatically translates this to...

You are calling the script wrong Bring up a cmd (command line prompt) and type: cd C:/Users/user/PycharmProjects/helloWorld/ module_using_sys.py we are arguments And you will get the correct output....

You can use the include tag in order to supply the included template with a consistent variable name: For example: parent.html <div class="row"> <div class="col-md-12 col-lg-12 block block-color-1"> {% include 'templates/child.html' with list_item=mylist.0 t=50 only %} </div> </div> child.html {{ list_item.text|truncatewords:t }} UPDATE: As spectras recommended, you can use the...

The values in the table are generated with the help of javascript being executed in the browser. One option to approach it is to automate a browser via selenium, e.g. a headless PhantomJS: >>> from selenium import webdriver >>> >>> driver = webdriver.PhantomJS() >>> driver.get("http://www.tabele-kalorii.pl/kalorie,Actimel-cytryna-miod-Danone.html") >>> >>> table = driver.find_element_by_xpath(u"//table[tbody/tr/td/h3...